Biology subjects

Venkatesh, K. V.

Publications and source records attributed to Venkatesh, K. V..

9 recordsLinked to original sources

bioRxiv2026

Ultrasensitive Regulation in the Tryptophan System in Escherichia coli Provides Effective Noise Mitigation

The tryptophan system in Escherichia coli maintains intracellular concentration of tryptophan in a narrow band regardless of the nutritional status and uncertainty in its environment. The system is characterized by three distinct regulations namely, genetic regulation, mRNA attenuation and enzyme inhibition, that use the tryptophan concentration as a feedback signal. It has been shown previously, that the multiple feedback loop design is responsible for rapid synthesis of tryptophan when faced with starvation. It is well known that a design with rapid response to external signals also implies poorer noise mitigation properties. This work investigates the design elements that limit the adverse impact of the multiple feedback loop architecture on noise propagation in the tryptophan system using a frequency response analysis. Specifically, we use sinusoidal input describing functions to approximate the transfer characteristics of the ultrasensitive regulators and then obtain the frequency response of the closed-loop feedback system. The study suggests that the tryptophan system of E. coli has evolved to simultaneously satisfy the two properties of rapid response and noise mitigation. Particularly, the multiple feedback loop is responsible for the rapid response, while the nonlinear regulation provides effective noise mitigation.

systems biology↗

bioRxiv2025

An integrated systems biology approach establishes arginine biosynthesis as a metabolic weakness in Candida albicans during host infection

Candida albicans (CAL), one of the leading causes of fungal infections affecting nearly 70% of the population, poses a significant global health threat. With the emergence of drug-resistant strains, mortality rates have reached a staggering 63.6% in severe cases, complicating treatment options and demanding the discovery of novel therapeutic targets. To address this pressing need, we employed a unique multidisciplinary approach to elucidate the metabolic pathways that enable CAL to switch from a commensal to a virulent state. Condition-specific genome-scale metabolic models (GSMMs), along with a novel integrated host-CAL model developed in this study, highlighted the central role of arginine (Arg) metabolism and uncovered ALT1, an arginine biosynthesis enzyme, as a critical metabolic vulnerability in CAL virulence. Heightened expression of arginine biosynthesis genes indicated that increased arginine synthesis mainly occurs through proline intermediates during host interaction. Significantly impaired virulence and in vivo pathogenicity of ALT1-deleted CAL highlighted the potential of targeting arginine metabolism as a novel strategy to combat antifungal resistance and underscored the power of integrating systems biology with experimental approaches in identifying new therapeutic targets. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=129 SRC="FIGDIR/small/632533v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@ac1b89org.highwire.dtl.DTLVardef@143c3d1org.highwire.dtl.DTLVardef@1ecfd26org.highwire.dtl.DTLVardef@1dfe98d_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2022

A systems biology approach to disentangle the direct and indirect effects of global transcription factors on gene expression in Escherichia coli

Delineating the pleiotropic effects of global transcriptional factors (TFs) is critical in understanding the system-wide regulatory response in a particular environment. Currently, with the availability of genome-wide TF binding and gene expression data for Escherichia coli, several gene targets can be assigned to the global TFs albeit inconsistently. Here, using a systematic integrated approach with emphasis on metabolism, we characterize and quantify the direct effects as well as the growth-rate mediated indirect effects of global TFs using deletion mutants of FNR, ArcA, and IHF regulators under glucose fermentative condition. Apart from the previous known metabolite-TF interactions, we predicted with high confidence several novel interactions arising from the allosteric effects of the intracellular metabolites. Our combined experimental and compendium level computational analyses revealed the co-expressed genes regulated by these TFs as well as the coordination of the direct and indirect target gene expressions in the context of the economy of intracellular metabolites. Besides, we extended our analysis to combinatorial deletions of these TFs to determine their cross-talk effects as well as conserved patterns of regulatory interactions. Overall, this study leverages the fundamentals of TF-driven regulation which could serve as a better template for deciphering mechanisms underlying complex phenotypes.

systems biology↗

bioRxiv2021

Mutant strains of Escherichia coli lacking global regulators, arcA and fis, demonstrate better growth fitness by pathway reprogramming under acetate metabolism

Global regulatory transcription factors play a significant role in controlling microbial metabolism under genetic and environmental perturbations. A systems-level effect of carbon sources such as acetate on microbial metabolism under disrupted global regulators has not been well established. Acetate is one of the substrates available in a range of nutrient niches such as the mammalian gut and high-fat diet. Therefore, investigating the study on acetate metabolism is highly significant. It is well known that the global regulators arcA and fis regulate acetate uptake genes in E. coli under glucose condition. In this study, we deciphered the growth and flux distribution of E.coli transcription regulatory knockout mutants {Delta}arcA, {Delta}fis and double deletion mutant, {Delta}arcAfis under acetate using 13C-Metabolic Flux Analysis which has not been investigated before. We observed that the mutants exhibited an expeditious growth rate (~1.2-1.6 fold) with a proportionate increase in acetate uptake rates compared to the wild-type. 13C-MFA displayed the distinct metabolic reprogramming of intracellular fluxes, which conferred an advantage of faster growth with better carbon usage in all the mutants. Under acetate metabolism, the mutants exhibited higher fluxes in the TCA cycle (~18-90%) and lower gluconeogenesis flux (~15-35%) with the proportional increase in growth rate. This study reveals a novel insight by stating the sub-optimality of the wild-type strain grown under acetate substrate aerobically. These mutant strains efficiently oxidize acetate to acetyl-CoA and therefore are potential candidates that can serve as a precursor for the biosynthesis of isoprenoids, biofuels, vitamins and various pharmaceutical products. ImportanceUnravelling the role of global regulatory genes on microbial metabolism of substrates available in various growth niche is important. Studies have shown that the global transcriptional regulators arcA and fis, under glucose availability, suppress the acetate uptake genes indicating a link between nutrient source and gene regulatory control. This work is focused on deciphering the influence of these regulators on acetate metabolism in E.coli. Growth studies using knockout strains ({Delta}arcA, {Delta}fis and {Delta}arcAfis) and 13C Metabolic flux analysis defined precise metabolic phenotypes under acetate metabolism. Interestingly, the mutants showed metabolic readjustment to facilitate optimal biomass requirements and a better balance between energy and precursor synthesis, resulting in better growth, which lacked in the wild-type strain. The outcomes of this study will be leveraged in understanding the regulatory control under various nutrient shifts.

microbiology↗

bioRxiv2021

Effect of ligand sensing on flagellar bundle formation in bacteria

E. coli swims in liquid media by rotating long appendages called flagella. The direction of rotation of each flagellum is governed by a transmembrane rotary nanomotor, which receives signals from ligand-specific receptors. Attractants bias the motor to rotate in CCW direction causing flagella to bundle and provide thrust for locomotion. Recent studies have shown that sensing not only leads to increase in CCW bias but also increases the motor rotation speed due to the recruitment of additional stator units bound to the rotor. Despite the detailed studies on bacterial motility, the effect of ligand sensing on the synchronization of flagellar filaments leading to bundle formation and changes in bundle geometry are not clear. In this work, we performed real-time imaging of the flagellar bundle of swimming cells in metabolising (glucose) and non-metabolisable (2-Deoxy-d-glucose) attractants. We characterized bundles during swimming by measuring visible distal length and the spread of filaments at poles. We show that sensing of attractant by receptor leads to the formation of tight bundles when compared to control buffer. Contrary to previous studies, the swimming speeds were proportional to the bundle tightness with the latter dependent not only on the bias but also on the torque exerted by the motor. We further show that the observed wiggles in the swimming trajectory of cells is directly proportional to the spread angles of bundle and is effected by both motor CCW bias and torque. Mutant cells, which were rendered non-motile due to the absence of the PTS (phosphotransferase system) sugar uptake mechanism, exhibited motility when exposed to the non-metabolisable attractant confirming that mere sensing can induce torque in flagellar motor. These results clarify the role of sensing and metabolism on bundle formation and its impact on the motility of cells. Statement of significancePeritrichously flagellated E. coli swims away or towards ligands by biasing the direction of rotation of its flagellar motor. Recently, it has been shown that motor speed is also modulated on merely sensing a ligand. How does this impact flagellar bundle formation and swimming behavior? Using real-time imaging, we show that the bundle geometry changes in response to both metabolisable and non-metabolisable ligand. Mere sensing of a ligand temporarily increases the motor torque and CCW bias that causes tight flagellar bundles and leads to smooth swimming trajectories at high speeds. Our result provides strong evidence of a new signalling pathway that controls the flagellar motor speed to enable the bacteria to respond efficiently to changes in its environment.

biophysics↗

bioRxiv2020

Global transcriptional regulators fine-tune the translational and metabolic machinery in Escherichia coli under anaerobic fermentation

Complex regulatory interactions between genetic and metabolic networks together confer robustness against external and internal perturbations in an organism such as Escherichia coli. In balanced exponential growth, this robustness is attributed to cost-effective metabolism by means of efficient resource allocation coordinated by the interplay of global transcriptional regulators with growth-rate dependent machinery. Here, we reappraise the role of global transcriptional regulators FNR, ArcA and IHF, integral to sustaining proteome-efficiency in anaerobic fermentative conditions, fundamental for optimal growth of E. coli. We reveal at the transcriptome and metabolome level, that absence of these global regulators ensued a disruption of nitrogen homeostasis, overexpression of otherwise unnecessary or hedging genes and impairment in core bottleneck steps and amino acid metabolism. Notably, our findings emphasize their importance in optimizing the metabolic proteome resources essential for rapid exponential growth. Consequentially, the perturbations in the metabolic proteome as a result of deletion of global regulators unbalances the ribosomal proteome share imposing a high translation program, though at the expense of lowered efficiency. We illustrate that disruption of this inherent trade-off between metabolic and ribosomal proteomic investment eventually culminate to lowered growth rates. Despite no changes in gene expression related to glucose import, our findings elucidate that the accumulations of intracellular metabolites directly modulated by growth rate, negatively impacts the glucose uptake. Our results employing the proteome allocation theory and quantitative experimental measurements, suffices to explain the physiological consequences of altered translational and metabolic efficiency in the cell, driven by the loss of these global regulators.

systems biology↗

bioRxiv2020

Elucidating the regulatory role of CRP in coordinating protein biosynthesis machinery with metabolism that defines growth optimality in Escherichia coli

Evolution entails the orchestration of cellular resources together with mutations to achieve fitter phenotypes. Here, we determined the system-wide pleiotropic effects that redress the significant perturbations caused by the deletion of global transcriptional regulator CRP in Escherichia coli when evolved in the presence of glucose. We elucidated that absence of CRP results in alterations in key metabolic pathways instrumental for the precise functioning of protein biosynthesis machinery that subsequently corroborated with intracellular metabolite profiles. Apart from acquiring mutations in the promoter of glucose transporter ptsG, the evolved populations recovered the metabolic pathways to their pre-perturbed state with amelioration of protein biosynthesis machinery coupled with fine-tuned proteome re-allocation that enabled growth recovery. However, ineffective utilization of carbon towards biomass as perceived from ATP maintenance flux and costly amino acid accumulations poses a limitation. Overall, we comprehensively illustrate the genetic and metabolic adjustments underlying adaptive evolvability, fundamental for understanding the growth physiology.

systems biology↗

bioRxiv2020

Ligand Sensing Enhances Bacterial Flagellar Motor Output via Stator Recruitment

The phenomenon of chemotaxis in bacteria, where the cells migrate towards or away from chemicals, has been extensively studied in the past. For flagellated bacteria such as Escherichia coli, a change in chemical concentration in its environment is sensed by a chemoreceptor and communicated via a well-characterised signalling pathway to the flagellar motor. It has been widely accepted that the signals change the rotation bias of the motor without influencing the motor speed. Here, we present results to the contrary and show that the bacteria is also capable of modulating motor speed on merely sensing a ligand. Step changes in concentration of non-metabolisable ligand cause temporary recruitment of stators leading to a momentary increase in motor speeds. For metabolisable ligand, the combined effect of sensing and metabolism leads to higher motor speeds for longer durations. Swimming speeds measured at the population level corroborate the observations. Experiments performed with mutant strains delineate the role of metabolism and sensing in the modulation of motor speed and show how speed changes along with changes in bias can significantly enhance bacterias response to changes in its environment.

biophysics↗

bioRxiv2019

\"Viscotaxis\" - Directed Migration of Mesenchymal Stem Cells in Response to Loss Modulus Gradient

Directed cell migration in response to chemical and mechanical gradients plays a crucial role in physiological and pathological conditions. One such mechanical cues that is known to influences cell migration is the gradient of substrate elastic modulus (E). However, the elastic modulus alone cannot fully define the material properties of the cellular microenvironment, which often has both elastic and viscous characteristics. In this study, we investigated the influence of the gradient of viscous nature, as defined by loss modulus, G\", on cell migration. We cultured human mesenchymal stem cells (hMSCs) on a collagen-coated polyacrylamide gel with constant elastic property, as defined by the storage modulus G, but with the gradient of loss modulus G\". We found hMSCs to migrate from high to low loss modulus. We have termed this, thus far unreported, directional cellular migration as \"Viscotaxis\". We have confirmed uniform collagen density and constant storage modulus of the gel by fluorescence microscopy and atomic force microscopy to eliminate the possibilities of haptotaxis and durotaxis. We hypothesize that material creep in the high loss modulus region hinders the building up of the cellular traction, leading to a force asymmetry that drives the observed viscotaxis. To verify our hypothesis, we estimated the cellular traction on gels with high and low loss moduli. We indeed found that cells apply higher traction force on more elastic materials i.e. materials with low loss modulus. On the disruption of actomyosin contractility with myosin inhibitor blebbistatin and ROCK inhibitor Y27632, directional migration was lost. Further, we showed that cells can maintain a stable morphology on a low loss modulus substrate but due to its inability to build up stable cellular traction on a substrate with high loss modulus, the cell spreading remains in a dynamic state. Our findings in this paper highlight the importance of considering the viscous modulus while preparing stiffness-based substrates for the field of tissue engineering.

biophysics↗